New Paper: ProteinsPlus: a comprehensive collection of web-based molecular modeling tools

4. Mai 2022

Foto: Katrin Schöning-Stierand

The ProteinsPlus (https://proteins.plus) web service is a steadily growing and developing collection of ready-to-use online tools for structure-based molecular design. We present novel developments and two newly incorporated tools in our most recent article in the web server issue of Nucleic Acids Research. Besides introducing novel functionalities of the tool GeoMine for textually, numerically and geometrically querying predicted and ligand-based binding sites in the PDB, we present JAMDA, a tool for fully automated molecular docking of small molecules in all structures of the Protein Data Bank (PDB). MicroMiner, a tool for mining for local single residue substitutions in the PDB, is also introduced and explained. Finally, we give an application example for analyzing AlphaFold protein structure models with our web service. We demonstrate how on-the-fly binding site comparison and molecular docking can assist in annotating the AlphaFold-predicted protein models with ligands. This might open new paths for binding site detection and function prediction for structurally previously unknown proteins. The publication including all details on these current developments is available as open access article at: https://academic.oup.com/nar/advance-article-abstract/doi/10.1093/nar/gkac305/6576358